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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcacacttgccaataggccattgaacagagcgtttggacattggataataaggcaattagtacatgtaaactaacctgctgggtgacttgggatcttgcagGTTTCGGTTGATTCATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGAAGAGTTGGCAATACTTGAGTTCCTGATTCAGCCTCAACCCAAGGAAGGTT

Basic information

species Vitis vinifera
transcript Vv19s0177g00280.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0177g00280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G13280.1 (Glycine max), 3'ss of exon 4
--gtatcacacttgccaataggccattgaacagagcgtttggacattggataataaggcaat-tagtacatgtaaactaacctgc-tgggtgacttgggatc-ttgcagGTTTCGGTTGATTCATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGAAGAGTTGGCAATACTTGAGTTCCTGATTCAGCCTCAACCCAAGGAAGGTT
   ||   |||||  |||| | | ||  ||   |   | ||||  |     ||||||  | | |  |  |  |  |  |   ||  ||  ||||    ||   |  |||||||| ||||| ||||| ||||| || ||||| || |||||||| |  ||||| ||| || | |||||||||||||| |||||||| || || || || |
gtatagtgcacttcacaat-gactatgtaatgaa---tgtggatctacttcaataagctactatgttgtagttgtaggagtatgagtgtatgacacaagaaaatctcagGTTTCTGTTGAGTCATGTCCAGTCAATTGCATACATTGGGTGGAGACAGAAGAATTGCCAGTGCTTGAGTTCCTGATCCAGCCTCAGCCGAAAGACGGGT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|351049165|gb|FQ449887.1|FQ449887
EST:     GGTGCGCAAGAGTCAAGGTTCAATATGGGGATGATGACAAGAAAATTGAG                         GTTTCGGTTGATTCATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGAA
genomic: GGTGCGCAAGAGTCAAGGTTCAATATGGAGATGATGACAAGAAAATTGAGgtatcacact ... gatcttgcagGTTTCGGTTGATTCATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGAA
EST: gi|351046176|gb|FQ442554.1|FQ442554
EST:     GGTGCGCAAGAGTCAAGGTTCAATATGGGGATGATGACAAGAAAATTGAG                         GTTTCGGTTGATTCATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGAA
genomic: GGTGCGCAAGAGTCAAGGTTCAATATGGAGATGATGACAAGAAAATTGAGgtatcacact ... gatcttgcagGTTTCGGTTGATTCATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGAA
EST: gi|352798834|gb|FQ478469.1|FQ478469
EST:     GGTGCGCAAGAGTCAAGGTTCAATATGGGGATGATGACAAGAAAATTGAG                         GTTTCGGTTGATTCATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGAA
genomic: GGTGCGCAAGAGTCAAGGTTCAATATGGAGATGATGACAAGAAAATTGAGgtatcacact ... gatcttgcagGTTTCGGTTGATTCATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGAA
EST: gi|34549898|gb|CF518130.1|CF518130
EST:     GGTGCGCAAGAGTCAAGGTTCAATATGGAGATGATGACAAGAAAATTGAG                         GTTTCGGTTGATTTCATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGA
genomic: GGTGCGCAAGAGTCAAGGTTCAATATGGAGATGATGACAAGAAAATTGAGgtatcacact ... gatcttgcagGTTTCGGTTGATT-CATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGA
EST: gi|351046175|gb|FQ442553.1|FQ442553
EST:     GGTGCGCAAGAGTCAAGGTTCAATATGGGGATGATGACAAGAAAATTGAG                         GTTTCGGTTGATTCATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGAA
genomic: GGTGCGCAAGAGTCAAGGTTCAATATGGAGATGATGACAAGAAAATTGAGgtatcacact ... gatcttgcagGTTTCGGTTGATTCATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGAA
EST: gi|352798343|gb|FQ480368.1|FQ480368
EST:     GGTGCGCAAGAGTCAAGGTTCAATATGGGGATGATGACAAGAAAATTGAG                         GTTTCGGTTGATTCATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGAA
genomic: GGTGCGCAAGAGTCAAGGTTCAATATGGAGATGATGACAAGAAAATTGAGgtatcacact ... gatcttgcagGTTTCGGTTGATTCATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataaggcaattagtacatgtaaactaacctgctgggtgacttgggatcttgcagGTTTCGGTTGATTCATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGAAGAGTTGGCAATACTTGAGTTCCTGATTCAGCCTCAACCCAAGGAAGGTT
                      aactaac  putative branch site (score: 1)
        aattagta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcacacttgccaataggccattgaacagagcgtttggacattggataataaggcaattagtacatgtaaactaacctgctgggtgacttgggatcttgcagGTTTCGGTTGATTCATGCCCAGTAAACTGCATTCACTGGGTGGATAGGGAAGAGTTGGCAATACTTGAGTTCCTGATTCAGCCTCAACCCAAGGAAGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA